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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gttcacagttttaggagtgaaatgtgttgttggcatgttcagaaactgaaaagagcacacttacgtgatgagatctaacaattatgcattatgatcgtagCTCGCAGCGCGGCTGAGAACATCCCGCCACGACCTCCTCCACGCGCTGCACCTAGAGCTGATGGCACTCTTCAACTTGACCAGAAATCTTTTCAGTTTCT

Basic information

species Physcomitrella patens
transcript PP1S42_16V6.1
intron # 2
splice site 3'
intron type U2

Mapped EST sequences

Showing partial alignments of ESTs and genomic sequences. See full alignments


 ATGC     EST sequence
 ATGC     genomic sequence (exon)
 ATGC     genomic sequence (truncated intron)


EST: gi|100395346|gb|BY953691.1|BY953691
EST:     TCCAAATATATCGGTTCATCAACGTCCAGCTGCTGCAGGGGCAAGCACAG                         CTCGCAGCGCGGCTGAGAACATCCCGCCACGACCTCCTCCACGCGCTGCAC
genomic: TCCAAATATATCGGTTCATCAACGTCCAGCTGCTGCAGGGGCAAGCACAGgtgcgcttca ... atgatcgtagCTCGCAGCGCGGCTGAGAACATCCCGCCACGACCTCCTCCACGCGCTGCAC
EST: gi|162231292|gb|FC406533.1|FC406533
EST:     TCCAAATATATCGGTTCATCAACGTCCAGCTGCTGCAGGGGCAAGCACAG                         CTCGCAGCGCGGCTGAGAACATCCCGCCACGACCTCCTCCACGCGCTGCAC
genomic: TCCAAATATATCGGTTCATCAACGTCCAGCTGCTGCAGGGGCAAGCACAGgtgcgcttca ... atgatcgtagCTCGCAGCGCGGCTGAGAACATCCCGCCACGACCTCCTCCACGCGCTGCAC
EST: gi|100426955|gb|BY977448.1|BY977448
EST:     TCCAAATATATCGGTTCATCAACGTCCAGCTGCTGCAGGGGCAAGCACAG                         CTCGCAGCGCGGCTGAGAACATCCCGCCACGACCTCCTCCACGCGCTGCAC
genomic: TCCAAATATATCGGTTCATCAACGTCCAGCTGCTGCAGGGGCAAGCACAGgtgcgcttca ... atgatcgtagCTCGCAGCGCGGCTGAGAACATCCCGCCACGACCTCCTCCACGCGCTGCAC
EST: gi|18328243|gb|BJ160247.1|BJ160247
EST:     TCCAAATATATCGGTTCATCAACGTCCAGCTGCTGCAGGGGCAAGCACAG                         CTCGCAGCGCGGCTGAGAACATCCCGCCACGACCTCCTCCACGCGCTGCAC
genomic: TCCAAATATATCGGTTCATCAACGTCCAGCTGCTGCAGGGGCAAGCACAGgtgcgcttca ... atgatcgtagCTCGCAGCGCGGCTGAGAACATCCCGCCACGACCTCCTCCACGCGCTGCAC
EST: gi|208363997|gb|DC939590.1|DC939590
EST:     TCCAAATATATCGGTTCATCAACGTCCAGCTGCTGCAGGGGCAAGCACAG                         CTCGCAGCGCGGCTGAGAACATCCCGCCACGACCTCCTCCACGCGCTGCAC
genomic: TCCAAATATATCGGTTCATCAACGTCCAGCTGCTGCAGGGGCAAGCACAGgtgcgcttca ... atgatcgtagCTCGCAGCGCGGCTGAGAACATCCCGCCACGACCTCCTCCACGCGCTGCAC
EST: gi|208376982|gb|DC911050.1|DC911050
EST:     TCCAAATATATCGGTTCATCAACGTCCAGCTGCTGCAGGGGCAAGCACAG                         CTCGCAGCGCGGCTGAGAACATCCCGCCACGACCTCCTCCACGCGCTGCAC
genomic: TCCAAATATATCGGTTCATCAACGTCCAGCTGCTGCAGGGGCAAGCACAGgtgcgcttca ... atgatcgtagCTCGCAGCGCGGCTGAGAACATCCCGCCACGACCTCCTCCACGCGCTGCAC
EST: gi|100423213|gb|BY958195.1|BY958195
EST:     TCCAAATATATCGGTTCATCAACGTCCAGCTGCTGCAGGGGCAAGCACAG                         CTCGCAGCGCGGCTGAGAACATCCCGCCACGACCTCCNTC-ACGCGCTGCA
genomic: TCCAAATATATCGGTTCATCAACGTCCAGCTGCTGCAGGGGCAAGCACAGgtgcgcttca ... atgatcgtagCTCGCAGCGCGGCTGAGAACATCCCGCCACGACCTCC-TCCACGCGCTGCA
EST: gi|100365178|gb|BY966849.1|BY966849
EST:     TCCAAATATATCGGTTCATCAACGTCCAGCTGCTGCAGGGGCAAGCACAG                         CTCGCAGCGCGGCTGAGAACATCCCGCCACGACCTCCTCCACGCGCTGCAC
genomic: TCCAAATATATCGGTTCATCAACGTCCAGCTGCTGCAGGGGCAAGCACAGgtgcgcttca ... atgatcgtagCTCGCAGCGCGGCTGAGAACATCCCGCCACGACCTCCTCCACGCGCTGCAC
EST: gi|100411477|gb|BY974655.1|BY974655
EST:     TCCAAATATATCGGTTCATCAACGTCCAGCTGCTGCAGGGGCAAGCACAG                         CTCGCAGCGCGGCTGAGAACATCCCGCCACGACCTCCTCCACGCGCTGCAC
genomic: TCCAAATATATCGGTTCATCAACGTCCAGCTGCTGCAGGGGCAAGCACAGgtgcgcttca ... atgatcgtagCTCGCAGCGCGGCTGAGAACATCCCGCCACGACCTCCTCCACGCGCTGCAC
EST: gi|100406431|gb|BY955623.1|BY955623
EST:     TCCAAATATATCGGTTCATCAACGTCCAGCTGCTGCAGGGGCAAGCACAG                         CTCGCAGCGCGGCTGAGAACATCCCGCCACGACCTCCTCCACGCGCTGCAC
genomic: TCCAAATATATCGGTTCATCAACGTCCAGCTGCTGCAGGGGCAAGCACAGgtgcgcttca ... atgatcgtagCTCGCAGCGCGGCTGAGAACATCCCGCCACGACCTCCTCCACGCGCTGCAC
EST: gi|100444442|gb|BY964140.1|BY964140
EST:     TCCAAATATATCGGTTCATCAACGTCCAGCTGCTGCAGGGGCAAGCACAG                         CTCGCAGCGCGGCTGAGAACATCCCGCCACGACCTCCTCCACGCGCTGCAC
genomic: TCCAAATATATCGGTTCATCAACGTCCAGCTGCTGCAGGGGCAAGCACAGgtgcgcttca ... atgatcgtagCTCGCAGCGCGGCTGAGAACATCCCGCCACGACCTCCTCCACGCGCTGCAC
EST: gi|7207567|gb|AW561615.1|AW561615
EST:     TCCAAATATATCGGTTCATCAACGTCCAGCTGCTGCAGGGGCAAGCACAG                         CTCGCAGCGCGGCTGAGAACATCCCGCCACGACCTCCTCCACGCGCTGCAC
genomic: TCCAAATATATCGGTTCATCAACGTCCAGCTGCTGCAGGGGCAAGCACAGgtgcgcttca ... atgatcgtagCTCGCAGCGCGGCTGAGAACATCCCGCCACGACCTCCTCCACGCGCTGCAC
EST: gi|100448633|gb|CJ972932.1|CJ972932
EST:     TCCAAATATATCGGTTCATCAACGTCCAGCTGCTGCAGGGGCAAGCACAG                         CTCGCAGCGCGGCTGAGAACATCCCGCCACGACCTCCTCCACGCGCTGCAC
genomic: TCCAAATATATCGGTTCATCAACGTCCAGCTGCTGCAGGGGCAAGCACAGgtgcgcttca ... atgatcgtagCTCGCAGCGCGGCTGAGAACATCCCGCCACGACCTCCTCCACGCGCTGCAC
EST: gi|18367244|gb|BJ199325.1|BJ199325
EST:     TCCAAATATATCGGTTCATCAACGTCCAGCTGCTGCAGGGGCAAGCACAG                         CTCGCAGCGCGGCTGAGAACATCCCGCCACGACCTCCTCCACGCGCTGCAC
genomic: TCCAAATATATCGGTTCATCAACGTCCAGCTGCTGCAGGGGCAAGCACAGgtgcgcttca ... atgatcgtagCTCGCAGCGCGGCTGAGAACATCCCGCCACGACCTCCTCCACGCGCTGCAC
EST: gi|100387757|gb|BY951757.1|BY951757
EST:     TCCAAATATATCGGTTCATCAACGTCCAGCTGCTGCAGGGGCAAGCACAG                         CTCGCAGCGCGGCTGAGAACATCCCGCCACGACCTCCTCCACGCGCTGCAC
genomic: TCCAAATATATCGGTTCATCAACGTCCAGCTGCTGCAGGGGCAAGCACAGgtgcgcttca ... atgatcgtagCTCGCAGCGCGGCTGAGAACATCCCGCCACGACCTCCTCCACGCGCTGCAC
EST: gi|18353836|gb|BJ185891.1|BJ185891
EST:     TCCAAATATATCGGTTCATCAACGTCCAGCTGCTGCAGGGGCAAGCACAG                         CTCGCAGCGCGGCTGAGAACATCCCGCCACGACCTCCTCCACGCGCTGCAC
genomic: TCCAAATATATCGGTTCATCAACGTCCAGCTGCTGCAGGGGCAAGCACAGgtgcgcttca ... atgatcgtagCTCGCAGCGCGGCTGAGAACATCCCGCCACGACCTCCTCCACGCGCTGCAC
EST: gi|18356924|gb|BJ188983.1|BJ188983
EST:     TCCAAATATATCGGTTCATCAACGTCCAGCTGCTGCAGGGGCAAGCACAG                         CTCGCAGCGCGGCTGAGAACATCCCGCCACGACCTCCTCCACGCGCTGCAC
genomic: TCCAAATATATCGGTTCATCAACGTCCAGCTGCTGCAGGGGCAAGCACAGgtgcgcttca ... atgatcgtagCTCGCAGCGCGGCTGAGAACATCCCGCCACGACCTCCTCCACGCGCTGCAC
EST: gi|100403625|gb|BY955020.1|BY955020
EST:     TCCAAATATATCGGTTCATCAACGTCCAGCTGCTGCAGGGGCAAGCACAG                         CTCGCAGCGCGGCTGAGAACATCCCGCCACGACCTCCTCCACGCGCTGCAC
genomic: TCCAAATATATCGGTTCATCAACGTCCAGCTGCTGCAGGGGCAAGCACAGgtgcgcttca ... atgatcgtagCTCGCAGCGCGGCTGAGAACATCCCGCCACGACCTCCTCCACGCGCTGCAC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctgaaaagagcacacttacgtgatgagatctaacaattatgcattatgatcgtagCTCGCAGCGCGGCTGAGAACATCCCGCCACGACCTCCTCCACGCGCTGCACCTAGAGCTGATGGCACTCTTCAACTTGACCAGAAATCTTTTCAGTTTCT
                           atctaac  putative branch site (score: 2)
                              taacaattat  TA-rich tract
















Putative cis-regulatory sequences

 atgc intron ATGC exonic elements by Pertea et al.
 ATGC exon atgc putative intronic elements
 ATGC putative exonic elements identified for retained introns
        10        20        30        40        50        60        70        80        90        100       110       120       130       140       150       160       170       180       190       200       210       220 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gttcacagttttaggagtgaaatgtgttgttggcatgttcagaaactgaaaagagcacacttacgtgatgagatctaacaattatgcattatgatcgtagCTCGCAGCGCGGCTGAGAACATCCCGCCACGACCTCCTCCACGCGCTGCACCTAGAGCTGATGGCACTCTTCAACTTGACCAGAAATCTTTTCAGTTTCT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCTGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGAT